Archive for the ‘other life’ Category
on free will and libertarianism 1: introducing some issues
I vaguely remember this book annoying me 35 years ago
Canto: So I’ve wanted to get back to this issue for some time, as it’s been on my mind, to connect an increasingly prevalent political ideology (or so it seems to me) with an increasingly tenuous philosophical position with regard to free will, but I’m not sure whether to start with the politics or the philosophy.
Jacinta: Well I think I can dispose of it all quite quickly. Free will’s a myth and individual freedom, however defined, has gotten us nowhere as a species. That’s it – so it’s off to the pub?
Canto: Well, that might be an interesting starting point, but I think we might need to put some flesh on the bones of those arguments, if I may cannibalise a cliché, or whatever.
Jacinta: Hmmm. So you really think there’s more to say?
Canto: Well I do feel the need to account for my change of position over several decades. Of course I’ve always been a determinist – the whole cause-effect relationship underpins our understanding of all human and non-human behaviour. I don’t think even quantum mechanics disrupts it too much, and to the extent it does, it certainly doesn’t do so in favour of human free will. But way back in the late seventies, when I was first introduced to the topic, ‘hard determinism’ as the term was then, was so out of fashion, and seemed to allow so little wiggle room for our actions, that I kind of assumed it was the province of attention-seeking extremists, or something. And of course it did seem a bit deflating to the human spirit, and all that.
Jacinta: So now you don’t mind a bit of deflation?
Canto: Well, over time, I reflected on my background, and perhaps also on the backgrounds of the philosophers and academics putting forward the compatibilist arguments – that somehow free will is compatible with determinism and even dependent on it. I found this later in Dennett’s book Elbow room, and I think there was some of it in Pinker’s The blank slate too. What I found was a kind of disdainful, and dare I say upper-middle class, attitude to ‘wrong-doers’ who need to be held accountable for their actions. And as a person who grew up in one of the most working-class and disadvantaged suburban regions in Australia, I felt defensive for the people around us (our family were better off than most), their bootlessness and despair. It certainly rubbed off on me in my teen years. I didn’t exactly bear a grudge against the world, but I certainly never had any inspiring teachers or adult figures who encouraged my scintillating intellect.
Jacinta: Okay, enough about you, what about the argument?
Canto: Well let’s look at free will first. The compatibilist argument is that free will is itself a determining factor in the decisions you make. You weigh the pros and cons in your mind, without undue influence from other sources, and determine to have tea with your breakfast instead of coffee, for the first time in months. Of course you’ve done this of your own free will, just as you’ve chosen to feed the dog instead of throwing her out of your 10th storey window, etc etc. The favourite term is ‘you could’ve done otherwise’.
Jacinta: But you didn’t.
Canto: And the feeling that you could’ve done otherwise is also determined, as is the feeling of regret that you quit that job when you should’ve stayed on, that you didn’t make that move interstate, that you didn’t keep in touch with person x, etc. The sense that we could have been better than what we are, could have done better than what we did, these are everyday feelings that we’re never free from. But getting back to compatibilists, they try to have the best of both worlds by claiming that the self is this autonomous determining factor in decision-making. It all revolves around this self. Presumably the developed self, since obviously the two-year-old self is not fully responsible for her actions.
Jacinta: Ah yes and there’s where it all falls apart. Where does this ‘self’ come from? We start as a fertilised egg, the width of a human hair. No brain, no heart, no belly, no skin, just genetic potential. Clearly we’re not making decisions. Nine months later, we’re born, fortunately with all those organs. But surely we’re not making our own decisions at this stage. And we’ve been subjected to a lot in this period, nutrients of all sorts, twists and turns, bumpings and grindings, the sounds of laughter, tears, music, shouts, squeals, long silences, all of which may influence our patterns of neural development both inside and outside the womb. All of which lay down the pattern of our future self, our future ‘free will’.
Canto: Yes, and from that time on its ‘meet the parents’, or caregivers, and/or our siblings and our homes, the furniture of our early lives. Not our choices. I think the no-free-will argument can be most persuasive when you can persuade the opposite side of the most obvious limitations, which are all big ones – for example you don’t get to choose your parents, your place or time of birth/conception, or even the species you were born into. So with those huge limitations accepted, you start to home in on the wiggle room the freewillers have left. Presuming they’re compatibilists, that’s to say determinists, they must accept that all that ultra-connecting and later trimming of neurons in early childhood has nothing to do with personal choice. And yet they try to argue that after all that connecting and trimming, when they’re a ‘fully determined self’, this self goes into auto mode, that of a self-determining self. Which presumably coincides with ‘adulthood’.
Jacinta: Right. As if our courts, or our laws, have solved the free will problem.
Canto: Yes, but it’s a bit like those claims for perpetual motion machines, that can produce output with no energy input. They’re as mythical as free will. The self is essentially only useful as an identifier, and it’s obviously very useful for that. And every self is unique, and perhaps that’s what confuses people. A person can be eccentric, ‘exceptionally different’, in good or bad ways, and we say ‘she’s really her own person’ or ‘she goes her own way’, and strictly speaking that can be said of everyone, whether human, fish or fowl, or of the plants on our balcony, or the jacarandas on our street, each one of which is unique, but not of their own free will.
Jacinta: We mistake complexity for free will, perhaps. Complexity is everywhere on this life-coated planet, but the human brain beats it all for complexity. We carry those things around, we feel it, and so we feel free, to possibly do anything, be anything, learn anything, commit anything. And feel proud when we do the ‘right’ thing, make the requisite effort and so on.
Canto: It’s arguable that this feeling of free will is important for our success. Or our striving. It’s up to you to work hard to pass that exam, to build a successful business, to become a regular in the first team, whatever. The sense of freedom can be exhilarating, though it might be just as obviously caused as the health-giving freedom ‘experienced’ by a plant moved from a nutrient-poor soil to a nutrient-rich one. Something in our environment makes us more successful than the guy down the road, or in Africa, but we don’t want to place too much emphasis on that environment, especially if we know we’ve put in an effort to succeed.
Jacinta: Okay, so what about punishment? As you’ve said, we might claim too much credit for our successes, isn’t a corollary that we place too much blame on those who ‘fail’, who give in to their peers’ world of violence and contempt? Punishment is mostly about deterrence, they say, but isn’t there a better way to treat people than this?
Canto: That’s an interesting question, and of course a complex one. We should talk about it next time.
a bonobo world 62: more species, and then back to the point of it all
male aggression – it’s everywhere
Canto: Okay, let’s look at other cetaceans. There are 89 species, so we can’t cover them all. There are toothed and baleen types, but all dolphins and porpoises are toothed. There are river dolphins and oceanic dolphins, and in terms of size, cetaceans range widely, so that we have names like northern right whale dolphin, southern right whale dolphin, false killer whale, pygmy killer whale and various types of humpback dolphin as well the humpback whale. So it might be that they’re as culturally various as humans. I’ll limit my examination, then, to four or five well-known species, with no pretence that any of them typify the whole.
Jacinta: Yes, when we talked about dolphins before, it was the common bottle-nose dolphin, right?
Canto: Essentially yes, and I’ll pick some of the best known cetaceans, avoiding those most endangered, because they’ll probably be the least studied in the wild. First, the humpback whale, which is a rorqual. Rorquals represent the largest group of baleen whales, and of course humpback whales are an iconic and fairly well researched species, as whales go. And one immediately interesting fact is that the females are on average slightly larger than the males.
Jacinta: Size usually matters.
Canto: And they can live up to 100 years. But let’s talk about sex, or courtship as the Wikipedia article on humpbacks charmingly describes it. You’ll be happy to know that humpbacks are polyandrous – that’s to say, females mate with many males during their breeding season. This is generally seen as the opposite of polygyny – one male mating with many females. In fact polyandry is more often seen in insects than in any other life forms. Humpbacks have even been known to have it off with other species. Wikipedia calls it hybridisation. There’s apparently a humpback-blue whale hybrid out there.
Jacinta: I assure you that when females rule the world – in nevereverland – any attempt to employ ‘euphemisms’ for fucking will be punished by instant castration.
Canto: Well you’ll also be amused to know that males fight over females.
Jacinta: How very unsurprising. But at least they sing, which almost compensates.
Canto: Yes, males and females vocalise, but the long, complex and very loud songs are produced by males. It’s believed that they help to produce estrus in the females.
Jacinta: The correct term is fuck-readiness.
Canto: In fact, researchers only think that because only males produce the complex songs. It’s a reasonable inference, but it could be wrong. Some think that the songs might be used to prove the male’s virility to the female, to make him more attractive. This supposedly happens with birdsong too.
Jacinta: Trying to think of human equivalents. Rocks in the jocks?
Canto: Oh no, too chafing. Being a good cook helps, I’ve found. But what with the obesity epidemic, that’s a balancing act. Anyway, those humpback boys put a lot of energy into their songs, which sometimes last for over 24 hours. Animals of one population, which can be very large, sing the same culturally transmitted song, which slowly changes over time. All interesting, but probably not much of a model for us. I can barely swim.
Jacinta: Well yes, it’s hardly sing or swim for us, but let’s turn to other cetaceans. What about blue whales?
Canto: Well it’s interesting to find that most websites don’t even mention their social life – it’s all about their ginormity, their big hearts, and their feeding and digestion. It took me a while to discover that they’re solitary creatures, which I suppose is common sense. Hard to imagine a superpod of blue whales out in search of a collective meal. They do sometimes gather in small groups, presumably for sex, and of course there’s a mother-calf relationship until maturity. As with humpbacks, the females are a bit larger than the males. What would that be about?
Jacinta: Well, some researchers (see link below) have discovered that male humpbacks favour the largest females, so there’s presumably sexual selection going on. And of course, they fight over the biggest females.
Canto: Well you can’t blame them for being macho. It be nature, and what do please gods.
Jacinta: Oh no, let’s not go there. Anyway, the largest females produce the largest and presumably healthiest offspring. They also found that the older females make the best mothers, which I’m sure is generally the case in humans too, mutatis mutandis.
Canto: So in conclusion, these mostly solitary creatures, whether they be cetaceans or primates, can’t be said to be patriarchal or matriarchal, but the males still manage to be more violent, or at least more cross with each other, than the females.
Jacinta: But it doesn’t have to be that way, hence bonobos.
Canto: Yes, but that makes me think. I hear that bonobos use sex to ‘ease tensions’, among other things. Tensions hints of violence, or at least anger. I’m wondering if that anger comes mostly from the males, and if the use of sex to dissipate that anger comes mostly from the females.
Jacinta: That’s a good question. There’s a site, linked below, which sort of looks at that question. It cites research showing that female bonobos gang up on male aggressors. The researchers found an absence of female-on-female aggression (perhaps less so than in the human world). According to this site – which may not be wholly reliable, as it’s really about humans and nightlife behaviour – female bonobos bond in small groups for the specific purpose of keeping males in line. How do they know that? They might be arguing from girl nightlife behaviour. I mean, who’s zoomin who?
Canto: The general point though is that among bonobos, males are more aggressive than females. Which isn’t to say that females can’t be aggressive, and not just in a defensive way.
Jacinta: This website also mentions something which is the general point of all our conversations on bonobos and humans and sex and well-being. It’s worth quoting in full:
Anthropological data analyzed by neuropsychologist James Prescott suggests societies that are more sexually open are also less likely to be violent. The key to understanding this correlation, however, is that it’s the society as a whole that is more sexually open and not just a small percentage of individuals.
Canto: That’s a good quote to get us back to humans. We need to look at this matter more closely next time. And the next and the next.
References
https://en.wikipedia.org/wiki/List_of_cetaceans
https://www.nbcnews.com/id/wbna29187881
Abiogenesis – LUCA, gradients, amino acids, chemical evolution, ATP and the RNA world
Jacinta: So now we’re thinking of the Earth 4 billion years BP, with an atmosphere we’re not quite sure of, and we want to explore the what and when of the first life forms. Haven’t we talked about this before?
Canto: Yeah we talked about the RNA world and viroids and abiogenesis, the gap between chemistry and biology, inter alia. This time we’re going to look more closely at the hunt for the earliest living things, and the environments they might’ve lived in.
Jacinta: And it started with one, it must have. LUA, or LUCA, the last universal common ancestor. Or the first, after a number of not-quite LUCAs, failed or only partially successful attempts. And finding LUCA would be much tougher than finding a viroid in a haystack, because you’re searching through an immensity of space and time.
Canto: But we’re much closer to finding it than in the past because we know so much more about what is common to all life forms.
Jacinta: Yes so are we looking definitely at the first DNA-based life form or are we probing the RNA world again?
Canto: I think we’ll set aside the world of viroids and viruses for now, because we want to look at the ancestor of all independently-existing life forms, and they’re all DNA-based. And we also know that LUCA used ATP. So now I’m going to quote from an essay by Michael Le Page in the volume of the New Scientist Collection called ‘Origin, Evolution, Extinction’:
How did LUCA make its ATP? Anyone designing life from scratch would probably make ATP using chemical reactions inside the cell. But that’s not how it is done. Instead energy from food or sunlight is used to power a protein ‘pump’ that shunts hydrogen ions – protons – out of the cell. This creates a difference in proton concentration, or a gradient, across the cell membrane. Protons then flow back into the cell through another protein embedded in the membrane, which uses the energy to produce ATP.
Jacinta: You understand that?
Canto: Sort of.
Jacinta: ‘Energy from food or sunlight is used..’ that’s a bit of a leap. What food? The food we eat is organic, made from living or formerly living stuff, but LUCA is the first living thing, its food must be purely chemical, not biological.
Canto: Of course, not a problem. I believe the microbes at hydrothermal vents live largely on hydrogen sulphide, and of course sunlight is energy for photosynthesising oganisms such as cyanobacteria.
Jacinta: Okay, so your simplest living organisms, or the simplest ones we know, get their energy by chemosynthesis, or photosynthesis. Its energy, or fuel, not food.
Canto: Semantics.
Jacinta: But there are other problems with this quote re abiogenesis. For example, it’s talking about pre-existent cells and cell membranes. So assuming that cells had to precede ATP.
Canto: No, he’s telling us how cells make ATP today. So we have to find, or synthesise, all the essential ingredients that make up the most basic life forms that we know – cell membranes, proteins, ATP and the like. And people are working towards this.
Jacinta: Yes and first of all they created these ‘building blocks of life’, as they always like to call them, amino acids, in the Miller-Urey experiments, since replicated many times over, but what exactly are nucleic acids? Are they the same things as nucleic acids?
Canto: Amino acids are about the simplest forms of organic compounds. It’s probably better to call them the building blocks of proteins. There are many different kinds, but generally each contain amine and carboxyl groups, that’s -NH2 and -COOH, together with a side chain, called an R group, which determines the type of amino acid. There’s a whole complicated lot of them and you could easily spend a whole lifetime fruitfully studying them. They’re important in cell structure and transport, all sorts of things. We’ve not only been able to create amino acids, but to combine them together into longer peptide chains. And we’ve also found large quantities of amino acids in meteorites such as the Murchison – as well as simple sugars and nitrogenous bases. In fact I think we’re gradually firming up the life-came from-space hypothesis.
Jacinta: But amino acids and proteins aren’t living entities, no matter how significant they are to living entities. We’ve never found living entities in space or beyond Earth. Your quote above suggests some of what we need. A boundary between outside and inside, a lipid or phospho-lipid boundary as I’ve heard it called, which must be semi-permeable to allow chemicals in on a very selective basis, as food or fuel.
Canto: I believe fatty acids formed the first membranes, not phospho-lipids. That’s important because we’ve found that fatty acids, which are made up of carbon, hydrogen and oxygen atoms joined together in a regular way, aren’t just built inside cells. There’s a very interesting video called What is Chemical Evolution?, produced by the Center for Chemical Evolution in the USA, that tells about this. Experimenters have heated up carbon monoxide and hydrogen along with many minerals common in the Earth’s crust and produced various carbon compounds including fatty acids. Obviously this could have and can still happen naturally on Earth, for example in the hot regions maybe below or certainly within the crust. It’s been found that large concentrations of fatty acids aggregate in warm water, creating a stable, ball-like configuration. This has to do with the attraction between the oxygen-carrying heads of fatty acids and the water molecules, and the repulsion of the carbon-carrying tails. The tails are forced together into a ball due to this repulsion, as the video shows.
fatty acids, with hydrophobic and hydrophilic ends, aggregating in solution
Jacinta: Yes it’s an intriguing video, and I’m almost feeling converted, especially as it goes further than aggregation due to these essentially electrical forces, but tries to find ways in which chemical structures evolve, so it tries to create a bridge between one type of evolution and another – the natural-selection type of evolution that operates upon reproducing organisms via mutation and selection, and the type of evolution that builds more complex and varied chemical structures from simpler compounds.
Canto: Yes but it’s not just the video that’s doing it, it’s the whole discipline or sub-branch of science called chemical evolution.
Jacinta: That’s right, it’s opening a window into that grey area between life and non-life and showing there’s a kind of space in our knowledge there that it would be exciting to try and fill, through observation and experimentation and testable hypotheses and the like. So the video, or the discipline, suggests that in chemical evolution, the highly complex process of reproduction through mitosis in eukaryotic cells or binary fission in prokaryotes is replaced by repetitive production, a simpler process that only takes place under certain limited conditions.
Canto: So under the right conditions the balls of fatty acids grow in number and themselves accumulate to form skins, and further forces – I think they’re hydrostatic forces – can cause the edges of these skins to fuse together to create ‘containers’, like vesicles inside cells.
Jacinta: So we’re talking about the creation of membranes, impermeable or semi-permeable, that can provide a safe haven for, whatever…
Canto: Yes, and at the end of the video, other self-assembling systems, such as proto-RNA, are intriguingly mentioned, so we might want to find out what’s known about that.
Jacinta: I think we’ll be doing a lot of reading and posting on this subject. I find it really fascinating. These limited conditions I mentioned – limited on today’s Earth surface, but not so much four billion years ago, include a reducing atmosphere lacking in free oxygen, and high temperatures, as well as a gradient – both a temperature gradient and a sort of molecular or chemical gradient, from more reducing to more oxidising you might say. These conditions exist today at hydrothermal vents, where archaebacteria are found, so researchers are naturally very interested in such environments, and in trying to replicate or simulate them.
Canto: And they’re interested in the boundary between chemical and biological evolution, and reproduction. There are so many interesting lines of inquiry, with RNA, with cell membranes….
Jacinta: Researchers are particularly interested in alkaline thermal vents, where alkaline fluids well up from beneath the sea floor at high temperatures. When this fluid hits the ocean water, minerals precipitate out and gradually create porous chimneys up to 60 metres high. They would’ve been rich in iron and sulphide, good for catalysing complex organic reactions, according to Le Page. The temperature gradients created would’ve favoured organic compounds and would’ve likely encouraged the building of complexity, so they may have been the sites in which the RNA world began, if it ever did.
a hydrothermal vent off the coast of New Zealand. Image from NOAA
Canto: So I think we should pursue this further. There are a lot of researchers homing in on this area, so I suspect further progress will be made soon.
Jacinta: Yes, we need to explore the exploitation of proton gradients, the development of proton pumps and the production of ATP, leaky membranes and a whole lot of other fun stuff.
Canto: I think we need to get our heads around ATP and its production too, because that looks pretty damn complex.
Jacinta: Next time maybe.
the unpredictable effects of permafrost thaw
This Aug. 12, 2009, photo shows a section of the vital Dempster Highway linking southern Canada with the Northwest Territories after it collapsed because warming temperatures caused the permafrost below to thaw. Permafrost melting from global warming is causing damage to infrastructure across the Arctic. (AP Photo/Rick Bowmer)
Canto: So what’s on the agenda for 2016 here at the new ussr?
Jacinta: Well I’m hoping we can do a ‘deep dive’, as one researcher likes to put it, on GMOs, another polarising subject, with a few posts, and maybe at least one on Monsanto, the supposedly evil capitalist monster that the anti-GMO crowd love crusading against…
Canto: Good, and I’d also like to focus a bit more on climate change, the ever-developing science of monitoring this complex beast, as well as the clean energy responses.
Jacinta: Including nuclear?
Canto: Well of course I don’t want to shy away from its potential, or its problems.
Jacinta: So no more black holes and cosmic webs?
Canto: I’d love to cover everything, if I had but talent enough, and time.
Jacinta: Yes and I’d like to find time for some philosophy as well, say on the limits of science, if any. But okay let’s get started on climate. I know you’ve been thinking about the ‘Climate Watch’ segment in the most recent issue of Cosmos, Australia’s most excellent science mag.
Canto: Yes, so while we’re congratulating our leaders (or not) on coming to an agreement re targets for global warming, we need to keep our eyes on the changes already underway, which many have been warning for years might lead to runaway, unstoppable warming.
Jacinta: Feedback loops and cascading effects.
Canto: Precisely, and one of the most serious, because unpredictable, changes we’re witnessing is in the arctic permafrost.
Jacinta: Which presumably is becoming less perma and frosty.
Canto: It’s thawing out, releasing large volumes of methane from the microbes that have been frozen there for many centuries.
Jacinta: And that’s a biggie in terms of greenhouse gases. So why do these presumably dead organisms release methane? I thought all our methane came from cow farts.
Canto: Did you really? Methane is released by rotting organic matter. You have peas in your freezer? Yes? So can you smell them? Very unlikely in their frozen state. So dig out a handful and stick them out in our summer sun. Pretty soon they’ll start to smell. What are you smelling?
Jacinta: Uhh, methane?
Canto: You’re quick. Amongst other gases of course – pure methane doesn’t stink like that. And because methane is such a potent greenhouse gas its release speeds up the thawing process, which could lead to a kind of tipping point, but the extent of this speeding up process, the amount of methane currently being released, and how it will affect the overall warming, these are horrendously difficult values to predict.
Jacinta: And methane’s essentially what we call natural gas isn’t it? CH4? So it’s another carbon-based product.
Canto: Yes, and twenty times more potent than CO2 as a greenhouse gas, according to climate scientists.
Jacinta: And the process we call rotting, that’s actually bacterial, isn’t it? Is it that these microbes release methane, inter alia, the way that we release CO2, after breathing in oxygen?
Canto: You’re talking about methanogens, which are actually archaea rather than bacteria. They thrive in anoxic, or low oxygen conditions, such as wetlands, but also in the digestive tracts of ruminants, indeed in most animals including humans. We release methane when we fart.
Jacinta: Some more than others. So I suppose the permafrost contains all these archaea, or they multiply when it starts to thaw?
Canto: They’re unlocked or reawakened by the thaw, and then, recent studies have shown, they can pump out methane at a phenomenal rate. And there’s a lot of permafrost involved at the moment, in land not under ice, including about half of Russia and Canada, and much of Alaska. They reckon there’s about 1.7 trillion tonnes of carbon trapped in this permafrost, twice the amount of atmospheric carbon.
Jacinta: So how much is likely to be released?
Canto: Nobody really has any idea, that’s the problem. One study has suggested that almost a tenth could be released by 2100, which doesn’t sound like much, but this effect hasn’t been factored in by the Intergovernmental Panel on Climate Change because it’s so hard to calculate – some of the microbes will be methanogens, some will be more liable to release CO2, depending on the local environments created by the thaw. Clearly it’ll be negative though, and will just add pressure and urgency to our plan to keep global warming down.
Jacinta: Yet I thought that the regions you mentioned, those permafrost regions, were full of evergreen forests – the taiga I think is the name. And they’re a carbon sink rather than a source of emissions.
Canto: You’re right, that’s another factor. In fact the taiga is a huge carbon sink, the biggest land sink on earth, but with climate change, the whole permafrost region is becoming less of a sink and more of an emitter, perhaps for the first time. The effects, as I’ve said are very difficult to predict, because the thaw is occurring at different rates, affecting different micro-climates, and with vastly different results even within metres. Being frozen has a uniform, more predictable effect. The thaw unlocks huge varieties of ecosytems – life in all its blooming buzzing confusion.
Jacinta: Well it does sound kind of fascinating in itself, apart from the disturbing effects…
Canto: Spoken like a true disinterested scientist.
permafrost thaw ponds around Hudson Bay, Canada
this one’s for the birds
Canto: If anybody doesn’t appreciate the beauty and complexity and general magnificence of birds they should pee off and never darken this blog again.
Jacinta: Right. Now what brought that on, mate?
Canto: Oh just a general statement of position vis-à-vis other species. Charles Darwin, an old friend of mine, was pretty disdainful of human specialness in his correspondence, but he kept a low profile – on this and everything else – in public. I want to be a bit more overt about these things. And one of the things that really amazes me about birds, apart from their physical beauty, is how much goes on in those teeny noggins of theirs.
Jacinta: Yes, but what really brought this on? I haven’t heard you rhapsodising about birds before.
Canto: You haven’t been inside my vast noggin mate. Actually I’ve been taking photos – or trying to – of the bird life around here; magpies, magpie-larks, crows, rainbow lorikeets, honeyeaters, galahs, corellas, sulphur-crested cockies, as well as the pelicans, black swans, cormorants, moorhens, coots and mallard ducks by the river, not to mention the ubiquitous Australian white ibis and the masked lapwing.
Jacinta: Well I didn’t know you cared. Of course I agree with you on the beauty of these beasties. Better than any tattoo I’ve seen. So you’re becoming a twitcher?
Canto: I wouldn’t go that far, but I’ve been nurturing my fledgling interest with a book on the sensory world of birds, called, appropriately, Bird sense, by a British biologist and bird specialist, Tim Birkhead. It’s divided into sections on the senses of birds – a very diverse set of creatures, it needs to be said. So we have vision, hearing, smell, taste, touch, and that wonderful magnetic sense that so much has been made of recently.
Jacinta: So we can’t generalise about birds, but I know at least some of them have great eyesight, as in ‘eyes like an eagle’.
Canto: Well, as it happens, our own Aussie wedge-tailed eagle has the most acute sense of vision of any creature so far recorded.
Jacinta: Well actually it isn’t ours, it just happens to inhabit the same land-form as us.
Canto: How pedantic, but how true. But Birkhead points out that there are horses for courses. Different birds have vision adapted for particular lifestyles. The wedge-tail’s eyes are perfectly adapted to the clear blue skies and bright light of our hinterland, but think of owl eyes. Notice how they both face forward? They’re mostly nocturnal and so they need good night vision. They’ve done light-detection experiments with tawny owls, which show that on the whole they could detect lower light levels than humans. They also have much larger eyes, compared with other birds. In fact their eyes are much the same size as ours, but with larger pupils, letting in more light. They’ve worked out, I don’t know how, that the image on an owl’s retina is about twice as bright as on the average human’s.
Jacinta: So their light-sensitivity is excellent, but visual acuity – not half so good as the wedge-tailed eagle’s?
wedge-tailed eagle – world’s acutest eyes
Canto: Right – natural selection is about adaptation to particular survival strategies within particular environments, and visual acuity isn’t so useful in the dark, when there’s only so much light around, and that’s why barn owls, who have about 100 times the light-sensitivity of pigeons, also happen to have very good hearing – handy for hunting in the dark, as there’s only so much you can see on a moonless night, no matter how sensitive your eyes are. They also learn to become familiar with obstacles by keeping to the same territory throughout their lives.
face of a barn owl – ‘one cannot help thinking of a sound-collecting device’, quoth researcher Masakazu Konishi
Jacinta: So they don’t echo-locate, do they?
Canto: No, though researchers now know of a number of species, such as oilbirds, that do. Barn owls, though, have asymmetrical ear-holes, one being higher in the head than the other, which helps them to pinpoint sound. It was once thought that they had infra-red vision, because of their ability to catch mice in apparently total darkness, but subsequent experiments have shown that it’s all about their hearing, in combination with vision.
Jacinta: Well you were talking about those amazing little brains of birds in general, and I must say I’ve heard some tales about their smarts, including how crows use cars to crack nuts for them, which must be true because it was in a David Attenborough program.
Canto: Yes, and they know how to drop their nuts near pedestrian crossings and traffic lights, so they can retrieve their crushed nuts safely. The genus Corvus, including ravens, crows and rooks, has been a fun target for investigation, and there’s plenty of material about their impressive abilities online.
seeing is believing
Jacinta: So what other tales do you have to tell, and can you shed any light on how all this cleverness comes in such small packages?
Canto: Well Birkhead has been studying guillemots for years. These are seabirds that congregate on cliff faces in the islands around Britain, and throughout northern Europe and Canada. They’re highly monogamous, and get very attached to each other, and thereby hangs another fascinating tale. They migrate south in the winter, and often get separated for lengthy periods, and it’s been noted that when they spot their partner returning, as a speck in the distance, they get highly excited and agitated, and the greeting ceremony when they get together is a joy to behold, apparently – though probably not as spectacular as that of gannets. Here’s the question, though – how the hell can they recognise their partner in the distance? Common guillemots breed in colonies, butt-to-butt, and certainly to us one guillemot looks pretty well identical to another. No creature could possibly have such acute vision, surely?
Jacinta: Is that a rhetorical question?
Canto: No no, but it has no answer, so far. It’s a mystery. It’s unlikely to be sight, or hearing, or smell, so what is it?
Jacinta: What about this magnetic sense? But that’s only about orientation for long flights, isn’t it?
Canto: Yes we might discuss that later, but though it’s obvious that birds are tuned into their own species much more than we are, the means by which they recognise individuals are unknown, though someone’s bound to devise an ingenious experiment that’ll further our knowledge.
Jacinta: Oh right, so something’s bound to turn up? Actually I wonder if the fact that people used to say that all Chinese look the same, which sounds absurd today, might one day be the case with birds – we’ll look back and think, how could we possibly have been so blind as to think all seagulls looked the same?
Canto: Hmmm, I think that would take a lot of evolving. Anyway, birds are not just monogamous (and anyway some species are way more monogamous than others, and they all like to have a bit on the side now and then) but they do, some of them, have distinctly sociable behaviours. Ever heard of allopreening?
Jacinta: No but I’ve heard the saying ‘birds of a feather flock together’ and that’s pretty sociable. Safety in numbers I suppose. But go on, enlighten me.
Canto: Well, allopreening just means mutual preening, and it usually occurs between mates – and I don’t mean in the Australian sense – but it’s also used for more general bonding within larger groups.
Jacinta: Like, checking each other out for fleas and such, like chimps?
Cant: Yeah, though this particular term is usually reserved for birds. Obviously it serves a hygienic purpose, but it also helps calm ruffled feathers when flocks of colonies live beak by jowl. And if you ever get close enough to see this, you’ll notice the preened bird goes all relaxed and has this eyes half-closed, blissed-out look on her face, but we can’t really say that coz it’s anthropomorphising, and who knows if they can experience real pleasure?
Jacinta: Yes, I very much doubt it – they can only experience fake pleasure, surely.
Canto: It’s only anecdotal evidence I suppose, but that ‘look’ of contentment when birds are snuggling together, the drooping air some adopt when they’ve lost a partner, as well as ‘bystander affiliation’, seen in members of the Corvus genus, all of these are highly suggestive of strong emotion.
Jacinta: Fuck it, let’s stop beating about the bush, of course they have emotions, it’s only human vested interest that says no, isn’t it? I mean it’s a lot easier to keep birds in tiny little cages for our convenience, and to burn their beaks off when they get stressed and aggressive with each other, than to admit they have feelings just a bit like our own, right? That might mean going to the awful effort of treating them with dignity.
Canto: Yyesss. Well on that note, we might make like the birds and flock off…
how the flock do they do that?
exoplanets – an introduction of sorts
Jacinta: So do you think we’ve hauled ourselves out of ignorance sufficiently to have a halfway stimulating discussion on exoplanets?
Canto: I think we should try, since it’s one of the most exciting and rapidly developing fields of inquiry at the moment.
Jacinta: And that’s saying something, what with microbiomes, homo naledi, nanobots and quantum biology…
Canto: Yes, enough to keep us chatting semi-ignorantly to the end of days. But let’s try to enlighten each other on exoplanets…
Jacinta: Extra solar planets, planets orbiting other stars, the first of which was discovered just over 20 years ago, and now, thanks largely to the Kepler Space Observatory, we’ve discovered thousands, and future missions, using TESS and the James Webb telescope, will uncover megatonnes more.
Canto: Yes, and you know, about the Kepler scope, l was blown away – this might be veering off topic a bit, but I was blown away in researching this by the fact that Kepler orbits the sun. I mean, I knew it was a space telescope, but I just assumed it was in orbit around earth, probably at a great distance to avoid interference from our atmosphere, but that we can position satellites in orbit around the sun, that really sort of stunned me, more I think than the exoplanet discoveries. Am I being naive?
Jacinta: No, not at all. Well, yes and no. Everything is stunning if you haven’t followed the incremental steps along the knowledge pathway. I mean, if you think, hey the sun’s a way away, and it’s really big and dangerous, best not go there, or something like that, you might be shocked, but think about it, we’ve been sending satellites around the earth for a long time now, and we know how to do it because we know about earth’s gravitational field and can calculate precisely how to harness it for satellite navigation. We’ve currently got a couple of thousand human-made satellites orbiting the earth and trying more or less successfully to avoid colliding with each other. So the sun also has a gravitational field and we’ve known the mathematics of gravitational fields since Newton. It’s the same formula for a star, a planet or whatever, all you need to know is its mass and its radius. And look at all the natural objects orbiting the sun without a problem. Can’t be that hard.
Canto: Okay… so how do we know the mass of the sun? Okay, forget it, let’s get back to exoplanets. What’s the big fuss here? Why are we so dead keen on exploring exoplanets?
Jacinta: Well the most obvious reason for the fuss is SETI, the search for extra-terrestrial intelligence, but to me it’s just satisfying a general curiosity, or you might say a many-faceted curiosity. And it’s all about us mostly. For example, is the solar system that we inhabit typical? We’ve mostly thought it was but we didn’t have anything to compare it with, but now we’re discovering all sorts of weird and wonderful planetary systems, and star systems, with gas giants like Jupiter orbiting incredibly close to their stars – it’s completely overturned our understanding of how planets exist and are formed, and that’s fantastically exciting.
Canto: So you say we discovered the first exoplanet about 20 years ago, and now we know about thousands – that’s a pretty huge expansion of our knowledge, so how come things have changed so fast? You’ve mentioned new technologies, new space probes, why have they suddenly become so successful?
Jacinta: Well I suppose it’s been a convergence of developments, but let’s go back to that first discovery, back in 1992. Two planets, the first ever discovered, were found orbiting a pulsar – a rapidly rotating neutron star. First discovery, first surprise. Pulsars with planets orbiting them, who would’ve thought? Pulsars are the remnants of supernovae – how could planets have survived that? But that first discovery was largely a consequence of our ability to measure, and the fact that pulsars pulse with extreme regularity. Any anomaly in the pulsing would be cause for further investigation, and that’s how the planets were found, and later independently confirmed. Now this was big news, in a field that was already becoming alert to the possibility of exoplanets, so you could say it opened the floodgates.
Canto: Really? But they didn’t discover any more for two or three years.
Jacinta: Well, okay it opened the gates but it didn’t start the flood, that really happened with the second discovery, the first discovery of a planet orbiting a main-sequence star like ours.
Canto: Main sequence? Please explain?
Jacinta: Well these are stars in a stable state, a state of balance or equilibrium, fusioning hydrogen – basically stars not too different from our own, within much the same range in terms of mass and luminosity. So 51 pegasus b was the first planet to be discovered by the radial velocity method, and radial velocity means the speed at which a star is moving towards or away from us. We can measure this, and whether the star is accelerating or decelerating in its movement, by means of the Doppler effect – waves bunch up when the object emitting them is moving towards us, they spread out when the object is receding from us, and the degree of the bunching or the spreading is a measure of their speed and whether it’s accelerating or decelerating. Now we can measure this with extreme accuracy using spectrometers, and that includes any perturbations in the star’s movement caused by orbiting bodies. That’s how 51 pegasus b was discovered.
Canto: So… how long have we had these spectrometers? Were they first developed in the nineties, or to the level of accuracy that they could detect these perturbations?
Jacinta: Well I don’t have a precise answer to that apart from the general observation that spectroscopes are getting better, and more carefully targeted for specific purposes. The French ELODIE spectrograph, for example, which was used to find 51 pegasus b, was first deployed in 1993 specifically for exoplanet searching, and since then it’s been replaced by another improved instrument, but of the same type. So it’s a kind of non-vicious circle, research leads to new technology which leads to new research and so on.
Canto: So – we’ve gotten very good at measuring perturbations in a star’s regular movements…
Jacinta: Regular perturbations.
Canto: And we know somehow that these are caused by planets orbiting around them? How do we know this?
Jacinta: Well we will know from the size of the perturbation and its regularity that it’s an orbiting body, and we know it’s not a star because it’s not emitting any light (though it may be a low-mass star whose light isn’t easily separated from its parent star). We also know – we knew from the results that it was a massive planet orbiting very close to its star – a hot Jupiter as they call it. And that was another surprise, but we’ve developed different techniques for discovering these things and we often use them to back each other up, to confirm or disconfirm previous findings. The ELODIE observation of 51 pegasus b was confirmed within a week of its announcement by another instrument, the Hamilton spectrograph in California. So there’s a lot of confirmation going on to weed out false positives.
Canto: So radial velocity is one technique, and obviously a very successful one as it got everyone excited about exoplanets, but what others are there, and which are the most successful and promising?
Jacinta: Well the radial velocity method was initially the most successful as you say, and hundreds of exoplanets have been discovered that way, but this method actually led to a kind of bias in the findings, because it was only able to detect perturbations above a certain level, so it was best for finding large planets close to their stars. But of course that was good too because we had never imagined that large gassy planets could exist so close to their stars. It’s opened up the whole field of planet formation. Then again, if the main aim is to find earth-like planets, this method is less effective than other methods. So let’s move on to the Kepler project. Kepler was launched in 2009, and since then you could say it has blitzed the field in terms of exoplanet detection. It uses transit photometry, which means that it measures the dimming of the light from a star when an orbiting planet passes between it and the Kepler detector.
Canto: So I get the idea of transit, as in the transit of venus, which we can see pretty clearly, but it’s amazing that we can detect transiting planets attached to stars so many light years away.
Jacinta: Well this is how we’ve expanded our world, from the infinitesimally small to the unfathomably large, from multiple billions of years to femtoseconds and beyond, through continuously refining technology, but let’s get back to Kepler. It orbits around the sun, and has collected data from around 145,000 main sequence stars in a fixed field of view – stars that are generally around the same distance from that dirty big black hole at the centre of our galaxy as our sun is.
Canto: Is that significant – that we’re focusing on stars in that range?
Jacinta: Apparently so, at least according to the Rare Earth Hypothesis, which puts all sorts of unimaginative limits on the likelihood of earth-like planets, IMHO, but no matter, it’s still a vast selection of stars, and we’ve reaped a grand harvest of planets from them – some 3000-odd, with over 1000 confirmed.
Canto: So… promising earth-like planets?
Jacinta: Yes, but I must point out that earth-like planets are difficult to detect. You see, Kepler was a kind of experiment, and we’ve learned from it, so that our next project will be much improved. For various reasons due to the photometric precision of the instrument, and inaccurate estimates of the variability of the stars in the field of view, we found that we needed to observe more transits to be sure we’d detected something. In other words we needed a longer mission than we’d planned for. And of course, Kepler has suffered serious technical problems, especially the failure of two reaction wheels, which have affected our ability to repoint the instrument. Having said that, we’ve been more than happy with its success.
Canto: Okay I just want to talk about these exoplanets. Can you summarise the most interesting discoveries?
Jacinta: Well, Kepler has certainly corrected the view we might’ve gotten from the earlier radial velocity method that large Jupiter-like planets are more common than smaller ones. We’ve had a number of reports from the Kepler group over the years, and over time they’ve adjusted downwards the average mass of the planets detected. And yes, they’ve discovered a number of planets in the ‘habzone’ as they call it. But that’s not all – only this year NASA confirmed the existence of five rocky planets, smaller than earth, orbiting a star that’s over 11 billion years old. I’m just trying to give you an idea of the explosion of findings, whether or not these planets contain life. And we’ve only just begun our hunt, and the refinement of instruments. It’s surely a great time to study astrophysics. It’s not just SETI, it’s about the incredible diversity of star systems, and working out where we fit into all this diversity.
Canto: Okay, I can see this an appropriately massive subject. Maybe we can revisit it from time to time?
Jacinta: Absolutely.
Some very useful sites:
http://www.planetary.org/explore/space-topics/exoplanets/
https://en.wikipedia.org/wiki/Kepler_(spacecraft)
how did life begin?: part 2 – RNA, panspermia, viroids and reviving the blob
Jacinta: So you’re going to talk about RNA, I know that stands for ribonucleic acid, and DNA is deoxy-ribonucleic acid, so – RNA is DNA without the oxygen?
Canto: Uhhh, you mean DNA is RNA without the oxygen.
Jacinta: Whatever, they’re big complex molecules aren’t they, but RNA is simpler, and less stable I think.
Canto: Okay, I’ll take it from here. We haven’t really known for very long that DNA is the essential material for coding and replicating life, and it’s a very complex molecule made up of four chemical bases, adenine, guanine, thymine and cytosine, better known as A, G, T and C. They connect to form base pairs, A always pairing with T and C with G.
Jacinta: What the hell are chemical bases? Do you mean bases as opposed to acids?
Canto: Well, yes. These bases, also called nucleobases, accept hydrogen ions, which have a positive charge. It’s all about pair bonding. The nucleobases – A, G, C and T, as well as uracil, found in RNA – are nitrogen-containing compounds which are attached to sugars… but let’s not get bogged down too much. The point is that DNA and RNA are nucleic acids that code for life, and most of the researchers chasing down the origin of life believe that RNA is a precursor of DNA in the process of replication.
Jacinta: And presumably there are precursors to RNA and so on.
Canto: Well presumably, but let’s just look at RNA, because we have a fair amount of evidence that this molecule preceded DNA as a ‘life-engine’, so to speak, and really no solid evidence, that I know of, of anything before RNA.
Jacinta: Okay so what is this evidence, and why did DNA take over?
Canto: Right, now the subject we’re entering into here is abiogenesis, the process by which life emerged from the inanimate. RNA is probably well down the chain from this emergence, but better to start with it than to dive into speculation. Now as you probably know, RNA has a single helical structure, and today it’s heavily involved in the process whereby DNA ‘creates’ proteins. In fact, all current life forms involve the action and interaction of three types of macromolecule, DNA, RNA and proteins…
Jacinta: But of course these complex molecules didn’t spring from nowhere.
Canto: Well we don’t know how they were built up, and many pundits think they may have been seeded here from elsewhere during the late heavy bombardment, which came to an end about 3.8 billion years ago, around the time that those Greenland rocks, with their heavy load of organic carbon, have been dated to. It seems plausible considering how quickly life seems to have taken off here.
Jacinta: Okay so tell us about RNA, how does it relate to the other two macromolecules?
Canto: Well, RNA is able to store genetic information, like DNA, and in fact it’s the genetic material for some of our scariest viruses, such as ebola, SARS, hep C, polio – not to mention influenza.
Jacinta: Wow, I didn’t know that. But one thing I do know about viruses is that they can’t exist independently of a host, so is RNA the basis of any truly independent life forms?
Canto: Not currently, on our planet, as far as we know, but the evidence is fairly strong that RNA has been central to life here from the very beginning, as it is still key to the most basic components of cells such as ribosomes, ATP and other co-enzymes. This suggests that RNA was once even more central, but in some areas it’s been subordinated to, and harnessed to, the more complex and recent DNA molecule. But, yes, since we can’t look at RNA coding for independent life-forms, we need to wind the clock back still further to look at precursors and other constituents of life, such as amino acids and peptides.
Jacinta: Which are chemical molecules, not biological ones. It seems to me we’re still a long way from working out the leap from chemistry to biology.
a peptide or amide bond – a covalent bond between two amino acid molecules
Canto: Yes, yes but we’re bridging various gaps. Peptides are created from amino acids, as you know. They are chains of amino acids linked by peptide bonds, and proteins are only distinguished from peptides in that they’re bigger versions of them, and bonded in a particular biologically useful way. You’ll notice when you read about this stuff that the terms ‘chemistry’ and ‘biology’ are used rather arbitrarily – a chemical compound can be referred to as a biological compound and vice versa. But various experiments have cast light on how increasingly ‘biological’ constituents are formed from simpler elements. For example, you may know that meteorites and comets, which bombarded the early earth in great numbers, contained plenty of amino acids – we’ve counted more than 70 different amino acids derived from meteorites, such as the Murchison meteorite that landed in Victoria in 1969. Another probable source of these amino acids, and even more complex and ‘biological’ molecules is comets, which also contain a lot of water in frozen form, but this has raised the question of how these molecules could have survived the impact of these colossal objects, which released enormous energy, some of them partially vaporising the earth’s crust. But an ingenious experiment, described in this video, and elsewhere, was able to simulate a comet’s impact, creating pressures many times greater than that experienced in our deepest oceans, to see what would happen to the amino acids. It was expected that they would barely survive the impact, but surprisingly they not only survived but forged bonds that created complex peptides.
a fragment of Murchison meteorite – of which there are many. This carbonaceous chondrite is still being analysed for organic compounds. Up to 70 amino acids identified so far
Jacinta: Mmmm, that is interesting. So, the gap between peptides, or proteins, and RNA, what do we know about that?
Canto: Well, now you’re getting into highly speculative territory, but it’s certainly worth speculating about. Firstly, though, in trying to solve this origin of life problem, we have to note that the earth’s atmosphere was incredibly different from what it is now. In fact it was probably quite different from the way Haldane and Oparin and later Miller and Urey envisaged it. It was predominantly carbon dioxide, with hydrogen sulphide, methane and other unpleasant gases – unpleasant to us, that is. That, together with the continual bombardment from outer space has led some scientists to suggest that the place to find the earliest life forms isn’t the open surface but in hidden nooks and crannies or deep underground, in more protected environments.
Jacinta: Yeah the discoveries of so-called extremophiles has made that idea fashionable, no doubt, but presumably these extremophiles are all DNA-based, so I don’t see how investigating them will answer my question.
Canto: Okay, so it’s back to RNA. The thing is, I don’t want to go into the properties of RNA here, it’s just too complicated.
Jacinta: I believe it was Richard Feynman who said something like ‘to fully understand a thing you have to build it’. So there’s still this leap from polypeptides or proteins, which don’t code for anything, they’re just built by ribosomes – RNA structures – from DNA instructions, to sophisticated coded replicators. We have no idea how DNA or RNA came into being, and nobody has successfully created life apart from Doktor Frankenstein. So it’s all a bit disappointing.
Canto: You must surely be joking, or just playing devil’s advocate. You know very well that this is an incredibly difficult nut to crack, and we’ve made huge progress, new discoveries are being made all the time in this field.
Jacinta: Okay, impress me.
Canto: Well, only this year NASA scientists have reported that the nucleobases uracil, thymine and cytosine, essential ingredients of DNA and RNA, have been created in the laboratory, from ingredients found only in outer space – for example pyramidine, which they’ve hypothesised was first created in giant red stars – and they’ve found pyrimidine in meteors. So, another step towards creating life, and further evidence that life here may have been seeded from elsewhere. And if that doesn’t impress you, what about viroids?
Jacinta: Uhhh… what are they, viral androids? Which reminds me, what about the artificial intelligence route to creating life? Intelligent life, what’s more exciting.
Canto: Another time. Viroids are described as ‘sub viral pathogens’. We were talking about viruses before, as a kind of halfway house between the living and the lifeless, but really they’re much more on the side of the living. The smallest known pathogenic virus is over 2000 nucleobases long, and the biggest – well, a megavirus was famously identified just last year and revived after being frozen in Siberian permafrost for something like 35,000 years…
Jacinta: An ancient megavirus has been revived…? WTF? Who thought that was a great idea? Wait a minute, the Siberian permafrost, wasn’t that where Steve MacQueen and his mates dropped The Blob? Megadeath, not just a shite band! We’re doomed!
Canto: Well, strictly speaking it’s a virion, a virus without a host, which means it’s in a kind of dormant phase, like a seed. But I don’t want to talk about megaviruses, fascinating though they are – and very new discoveries. I want to talk about viroids, which are plant pathogens. They consist of short strands of RNA, only a few hundred nucleases long, without the protein coat that characterises viruses, and their existence tends to support the ‘RNA world hypothesis’. It was the discoverer and namer of viroids, Theodor Diener, who pointed out that they were vitally important macromolecules for explaining essential steps in the evolution of life from inanimate matter. That was back in 1989, but his remarks were ignored, and only rediscovered in 2014. So viroids are now a big focus in abiogenesis. They’ve even been called living relics of the pre-cellular RNA world.
Jacinta: Okay, I’m more or less impressed. We’ll have to do more on abiogenesis in the future, it’s an intriguing topic, with more breakthroughs in the offing it seems. ..
how did life begin? part 1 – Greenland rocks, warm little ponds and unpromising gunk
the basics of the Miller-Urey experiment: sparking interest
Jacinta: Well, we need an antidote to all that theological hocus-pocus, so how about a bit of fundamental science for dummies?
Canto: Sounds great, I just happened to read today that there are three great questions, or areas of exploration for fundamental science. The origin of the universe – and its composition, including weird black holes, dark matter and dark energy – that’s one. The others are the origin of life and the origin of consciousness. Take your pick.
Jacinta: I’ll choose life thanks.
Canto: Not a bad choice for a nihilist. So life has inhabited this planet for about three and a half billion years, or maybe more, while the planet was still cooling from its formation…
Jacinta: Isn’t it still doing that?
Canto: Well, yes of course. An interesting study conducted a few years ago found that around 54% of the heat welling up from within the earth is radiogenic, meaning that it results from radioactive decay of elements like radium and thorium. The rest is primordial heat from the time of the planet’s coalescing into a big ball of matter.
Jacinta: Gravity sucks.
Canto: Energetically so.
Jacinta: You say three and a half billion years or more – can you be a bit more specific? Are we able to home in on the where and the when of life’s origin on this planet?
Canto: Well, that would be the pot of gold, to locate the place and time of the first homeostatic replicators, to wind back history to actually witness that emergence, but I suspect there would be nothing to actually see, at least not on the time-scale of a human life. I think it’d be like the emergence of human language, only slower. You’d have to compress time somehow to witness it.
Jacinta: Fair enough, or maybe not, it seems to me that the distinction between the animate and the inanimate would be pretty clear-cut, but anyway presumably scientists have a time-frame on this emergence. What allows them to date it back to a specific time?
Canto: Well, it’s an ongoing process of honing the techniques and discovering more bits of evidence, a bit like what has happened with defining the age of our universe. For example, you’ve heard of stromatolites?
Jacinta: Yes, those funny black piles that stick out of the water and sand, somewhere in Western Australia? They’re made from really old fossilised cyanobacteria, right?
Canto: Well, that’s a start, they’re rather more complicated than that and we’re still learning about them and still discovering new deposits, all around the world, both on the shoreline and inland. But the Shark Bay stromatolites in WA were the first to be identified, and that was only in 1956. More recently though, there’s been an entirely different discovery in Greenland that’s raised a lot of excitement and controversy…
Jacinta: But hang on, these stromatolites, they say they’re really old, like more than 3 billion years, but how do they know that? As Bill Bryson would say.
Canto: Well, good question Jass, in fact it’s highly relevant to this Greenland discovery so let me talk about radiometric dating, using this example. Greenland has been attracting attention since the sixties as a potential mineral and mining resource, so the Danish Geological Survey was having a look-see around the region of Nuuk, the capital, in the south-west of the island. The principal geologist found ten successive layers of rock in the area, using standard stratigraphic techniques that you can find online, though they’re not always easy to apply, as strata are rarely neatly horizontal, what with crustal movements, fault-lines and rockfalls and erosion and such. Anyway, it was his educated guess that the bottom of these layers was extremely old, so he sent a sample to Oxford, to an expert in radiometric dating there. This was in about 1970.
Isua rocks, Greenland. Oldest rocks discovered, showing plausible traces of 3.8 billion-year-old life
Jacinta: And doesn’t it have to do with radioactive isotopes and half-lives and such?
Canto: Absolutely. Take uranium 238, which if you’ve been watching the excellent recent ABC documentary you’ll know that it decays through a whole chain of, from memory, twelve nuclides before stabilising as an isotope of lead. That decay has a half-life of 4.5 billion years – longer than the life of this planet, or at least the life of its crust. So it’s a matter of measuring the ratio of isotopes, to see how much of the natural uranium has decayed. In this case, the gneiss, the piece of bottom-strata rock that was analysed, had the highest proportion of lead in it of any naturally occurring rock ever discovered.
Jacinta: So that means it’s likely the oldest rock? Aw, I thought Australia had the oldest. This is terrible news.
Canto: No time to be parochial when the meaning of life is at stake. May I continue? So this was an exciting discovery, but more was to come, and it’s continuing to come. The geological team were inspired to continue their explorations around the Godthaab Fjord in Greenland, and found what are called ‘mud volcanoes’, pillows of basaltic volcanic lava that had issued out into the seawater. These were again dated at about 3.7 billion years old, and this strongly suggested the existence of warm oceans at that time, with hydrothermal vents such as those recently discovered to be teeming with life…
Jacinta: Right, so that might be pushing the age of life back a few hundred million years, if it can be verified, but it still doesn’t answer the how question..
Canto: Oh, nowhere near it, but I’ve just started mate. May I continue? Not surprisingly this region is now seen as a treasure trove for those hunting out the first life forms and trying to work out how life began. It was soon found that the Isua greenstone to the north of Nuuk contains carbon with a scientifically exciting isotopic ratio. The level of carbon 13 was unexpectedly low. This is generally an indication of the presence of organic material. Photosynthesising organisms prefer the lighter carbon 12 isotope, which they capture from atmospheric or oceanic carbon dioxide. But the finding’s controversial. Many are skeptical because this is the period known as the ‘late heavy bombardment’, with asteroids crashing and smashing and vaporising and possibly even sterilising… and they haven’t discovered any fossils.
Jacinta: So, photosynthesis, that’s what created the great oxygenation, which created an atmosphere for complex oxygen-dependent organisms, is that right?
Canto: Well, that was much later, and it’s a vastly complex story with quite a few gaps in it, so maybe we’ll save it for future conversations…
Jacinta: Okay, fine, but couldn’t one of those asteroids have brought life here, or proto-life, or the last essential ingredient…?
Canto: Yes, yes, maybe, but you’re distracting me. May I please continue? Where was I? Okay, so let’s look at the various theories put forward about the origin of life – and it will bring us back to Greenland. You’ve mentioned one, called panspermia. That’s the idea that life was seeded here from space, maybe during the heavy bombardment…
Jacinta: Which isn’t an adequate explanation at all, because where did that life come from? I want to know how any life-form anywhere can spring from the inanimate.
Canto: Yes all right, don’t we all smarty-pants? One of the most interesting early speculators on the subject was one Charles Darwin, who wrote – very famously – in a letter to his good mate Joseph Hooker in 1871, and I quote:
It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present.— But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity &c present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.
Now this was pretty damn good speculation for the time, and a couple of generations later two biologists, Aleksandr Oparin of Russia and John Haldane of England, independently developed a hypothesis that built on Darwin’s ideas.
Jacinta: Oh yes, they had this idea that if you added a bit of lightning to the early terrestrial atmosphere, which was full of ammonia or something, you’d get a lot of organic chemistry happening.
Canto: Well I think the ‘or something’ part is true there – their idea was that there was a lot of hydrogen, methane and water vapour in the early atmosphere, and that, combined with local heat caused perhaps by lightning, or volcanic activity or some sort of concentrated solar radiation, the combo created a soup of organic compounds, out of which somehow over time emerged a primordial replicator.
Jacinta: So far, so vague.
Canto: Okay, I’m just getting started. The Oparin-Haldane hypothesis was highly speculative, of course. The point being made was that this key event was all that was needed for natural selection to kick in. This replication must have been advantageous, and of course over time there would’ve been mutations,with the mutants competing with the originals, and the winners would’ve been the most efficient and effective harvesters of resources, and there would’ve been expansion and more mutations and modifications and so forth. And out of that would come the first self-sustaining homeostatic environment, the proto-cell, within which more sophisticated machinery for processing resources could be developed…
Jacinta: Okay so you’ve more or less succeeded in dissolving the boundary between the animate and the inanimate before my eyes, but it’s still pretty vague on the details.
Canto: In 1953, Stanley Miller took up the challenge of his supervisor, famous Nobel Prize-winning biologist Harold Urey, who noted that nobody had tested the Oparin-Haldane hypothesis experimentally. Miller created a mini-atmosphere in a bottle, using methane (CH4), hydrogen, water vapour and ammonia (NH3), and after sparking it up for a while, he managed, to the amazement of all, to produce amino acids, the building blocks of proteins. Surely the first step in producing life itself.
Jacinta: Ah yes, that was a famous experiment, but didn’t it turn out to be something of a dead end?
Canto: Well, yes and no. It has been replicated with different mixtures and ratios of gases, and amino acids, sugars and even traces of nucleic acids have been generated, but nothing that could be described as a primordial replicator. But of course this work has got a lot of biologists thinking.
Jacinta: But this was 60 years ago. That’s a lot of thought without much action.
Canto: Well, what has since been realised about the experiments of Miller and others is that they create an enormous complexity of organic molecules in a rather uncontrolled way, a kind of chemical gunk similar to what might be created when you burn the dinner. The point being that when you burn the dinner – which is something necessarily organic like a dead chook, or pig, or tragically finless shark or whatnot…
Jacinta: Or a pumpkin, or Nan’s rhubarb pie..
Canto: Yeah, okay – you get this messy complexity, all mixed with oil and vinegary acids and shite – you get this break-down into gunk, and that’s easy. What’s hard is to go in the other direction, to build up from gunk into a fully fledged chicken, or a handsomely finned shark. And that’s what these experiments were trying to do, in their small way. They were creating this primordial-soup-gunk and hoping, with a bit of experimental help, to spark life into it, and basically getting nowhere. The problem is essentially to do with randomness and order. How do we get order out of random complexity? It’s easy to go the other way, for example with explosions and machine guns and such. We see that everywhere. But building the kind of replicating order that you find even in mycoplasma, the smallest genus of bacteria, from scratch, and by chance – well, that’s mind-bogglingly improbable.
mycoplasma, one of the simplest life forms – but try making one from scratch
Jacinta: So we have to think in terms of intermediate stages.
Canto: Yes, well, there are big problems with that, too… But let’s give it a rest for now. Next time, we’ll discuss the RNA world that most biologists are convinced preceded and helped create the DNA world we live in.
N B – This piece owes much to many, but mainly to Life on the edge: the coming of age of quantum biology, by Jim Al-Khalili & Johnjoe McFadden
the anthropic principle lives on and on
The anthropic principle, the idea that the universe – and let’s not muddle up our heads with multiverses – appears to be tweaked just right, in a variety of ways, for the existence and flourishing of humans, has long been popular with the religious, those invested in the idea of human specialness, a specialness which evokes guided evolution, both in the biological and the cosmological sense. And, of course, God is our guide.
Wikipedia, God bless it, does an excellent job with the principle, introducing it straight off as the obvious fact that anyone able to ascertain the various parameters of the universe must necessarily be living in a universe, or a particular part of it, that enables her to do the ascertaining. In other words the human specialness mob have it arse backwards.
So I’ll happily refer all those questing to understand the anthropic principle, in strong and weak forms, it proponents and critics, etc, to Wikipedia. I’ve been brought to reflect on it again by my reading of Stephen Jay Gould’s essay, ‘mind and supermind’, in his 1985 collection, The Flamingo’s Smile.
Yes, the anthropic principle, which many tend to think is a clever new tool for deists, invented by the very materialists who dismiss the idea of supernatural agency as unscientific, is an old idea – much more than 30 years old, because Gould was critiquing not only Freeman Dyson’s reflections on it in the eighties, but those of Alfred Russel Wallace more than a century ago, in his 1903 book Man’s Place in the Universe. Gould had good reason for comparing Dyson and Wallace; their speculations, almost a century apart, were based on vastly different understandings of the universe. It reminds us that our understanding of the universe, or that of the best cosmologists, continues to develop, and, I strongly suspect, will never be settled.
Theories and debates about our universe, or multiverse, its shape and properties, are more common, and fascinating, than ever, and accompanied by enough mathematics to make my brain bleed. The other day one of my regular emails from Huff Po science declared that maybe the universe didn’t have a beginning after all. This apparently from some scientists trying to grab attention in a pretty noisy field. I’ve only scanned the piece, which I would hardly be qualified to pass judgment on. But not long ago I read The Unknown Universe, a collection of essays from New Scientist magazine, dedicated to all ideas cosmological. I didn’t understand all of it of course, but genuine questions were raised about whether the universe is finite or infinite, about whether we really understand the time dimension, about how the laws that govern the universe came into being, and many other fundamental concepts. It’s interesting then to look back to more than a century ago, before Einstein, quantum mechanics, and space probes, and to reflect on the scientific understanding of the universe at that time.
A version of the universe, based on Lord Kelvin’s calculations, used by Wallace
In Wallace’s time (a rather vague term because the great scientist’s life spanned 90 years, which saw substantial developments in astronomy) the universe, though considered almost unimaginably massive, was calculated to be much smaller than today’s reckoning. According to a diagram in Man’s Place in the Universe, it ended a little outside the Milky Way galaxy, because we had no tools at the time to measure any further, though Lord Kelvin, the dominant figure in physics and astronomy in the late 19th century, made a number of dodgy calculations that were taken seriously at the time. In fact, Kelvin’s figures for the size of the universe, and for the age of the earth, though too small by orders of magnitude, were considered outrageously huge by most of his contemporaries; but they at least began to accustom the educated public to the idea of ginormity in space and time.
But size wasn’t of course the only thing that made the universe of that time so different from our own conceptions. The universe of Wallace’s imagination was stable, timeless, and, to Wallace’s mind, lifeless, apart of course from our planet. However, he doesn’t appear to have any good argument for this, only improbability. And an odd kind of hope, that we are unique. This hope is revealed in a passage of his book where he goes off the scientific rails just a bit, in a paean to our gloriously unique humanity. A plurality of intelligent life-forms in the universe
… would imply that to produce the living soul in the marvellous and glorious body of man – man with his faculties, his aspirations, his powers for good and evil – that this was an easy matter which could be brought about anywhere, in any world. It would imply man is an animal and nothing more, is of no importance in the universe, needed no great preparations for his advent, only, perhaps, a second-rate demon, and a third or fourth-rate earth.
Wallace, though by no means Christian, was given to ‘spiritualism’, souls and the supernatural, all in relation to humans exclusively. That’s to say, he was wedded to ‘human specialness’, somewhat surprisingly for his theory of evolution by wholly natural selection from random variation. This is the chain, it seems, that links him to modern clingers-to the anthropic principle, such as William Lane Craig and his epigones, who must needs believe in a value-laden universe, with their god as the source of value, and we humans, platonically created as the feeble facsimiles of the godhead, struggling to achieve enlightenment in the form of closeness to the Creator, with its appropriate heavenly rewards. And so we have such typical WL Craigisms as ‘God is the best explanation of moral agents who apprehend necessary moral truths’, ‘God is the best explanation of why there are self-aware beings’ and ‘God is the best explanation of the discoverability of the universe [by humans of course]’. These best explanation ‘arguments’ can be added to ad nauseum, of course, for they’re all of a part, and all connected to the Wallace quote above. We’re special, we must be special, we must be central to the creator’s plan, and our amazingness, our so-much-more-than-animalness, in spite of our many flaws, suggests a truly amazing creator, who made all this just for us.
That’s the hope, captured well by the great French biologist Jaques Monod when he wrote
All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its contingency.
I think modern philosophy has largely moved on from desperate denialism, but Monod’s remarks certainly hold true for religions, past present and future. Basically, the denial of our contingency is the central business of religion. It’s hardly surprising then that the relationship between religion and science is uneasy at best, and antagonistic at its heart. The multiverse could surely be described as religion’s worst nightmare. But that’s another story.
some interesting beasties: cheetahs
Sadly I don’t have so much time for writing these days, especially anything too strenuous or research-based, so I think I’ll do a series on organisms that have interested me over the years – or that I’ve just recently been fascinated by, for that matter.
Over at Not Exactly Rocket Science, there’s an article to whet the appetite as well as to apply a corrective to our thinking about everyone’s favourite wild cat, the cheetah (the name derives from Sanskrit, and cheetahs are found in Iran as well as Africa, and were probably more widespread in Asia in earlier times). Cheetahs are a vulnerable species, with about 10,000 of them currently existing in the wild. They’re described as a ‘charismatic species’, meaning that they’re utilised a lot as ‘ambassadors’ to draw attention to environmental and habitat issues for wildlife in general – along with elephants, humpback whales, giant pandas, California condors, grey wolves and such.
Cheetahs are, of course, built for speed in every way, though agility, with an incredible acceleration and deceleration rate, is also a key to their success. They can accelerate from zero to 40mph in just three strides – faster than the most sophisticated racing cars. Claims that their lightning runs leave them half-dead with heat exhaustion much of the time are, however, wildly exaggerated, as are the claims that they lose as much as half of their kills to lions and hyenas. In fact, cheetahs use up far more of their energy seeking out or tracking down potential kills than they do actually chasing them. A cheetah sprint takes up only 45 seconds a day on average – that’s less time than I spend on my high intensity interval training.
The key to maintaining cheetahs in the wild, then, is not to add to their greatest and most energy-sapping problem: finding food. Adding obstacles to their habitat, such as fences and enclosures, and depleting that habitat of their favourite food – gazelle, deer and impala, and the odd young zebra or springbok – would make life that bit more painful for them.
Speed, of course, is the cheetah’s big specialisation, what it’s adapted for. In fact over-specialisation is arguably its main problem, as it doesn’t have the bulk or strength to fight off other predatory mammals, all of which annoyingly compete for the same food. It’s light, with a weight that averages around 50 kgs, and its aerodynamically evolved head and body trade speed for strength, meaning that its jaws and teeth don’t have the size or force of other wild cats. It has a flattened ribcage but larger than usual heart and lungs for large intakes of air and fast pumping of blood. It also has a longer and larger tail than most cats, which it uses as a rudder for balance as it sets off on one of its twisting and turning runs. Its claws are only semi-retractable, unlike those of most cats (its genus name, Acinonyx, is Greek for ‘no-move claw’). This gives it extra grip while running. Males and females are the same size and hard to tell apart from distance.
Cheetahs don’t roar but they make up for it with a range of other noises, including purring like a – well, a cat, when experiencing domestic plenitude. They also hiss, spit, growl and even yowl when faced with danger. Cubs make a bird-like chirping sound, and the mother makes a similar sound when trying to locate her young. A sound called churring – no idea what that sounds like – is used on social and sexual occasions between adults. Male cheetahs form lifelong partnerships, often but not always with brothers, while females are solitary, bringing the kids up by themselves. They tend to mate with a variety of males – which hardly makes it mating, really. Interestingly, though the females are regular hunters, they’re not territorial, unlike the males, who practice group territoriality, each member of the gang contributing his scent.
Female cheetahs put their kids – or those that survive, as there’s a heavy infant mortality rate – through a tough survival training schedule before abandoning them at around 18 months. At around 2 years of age the females go their lonesome ways and the males hang together, sometimes combining with other blokes. It seems to work for them. In fact I think I read somewhere that males live longer on average than females, which wouldn’t surprise me. Fending for yourself all the time’s a deadly business, even when it’s all laid on in the big smoke, never mind having to chase your meals every day into old age. So spare a thought for the cheetahs, especially the girls, under-appreciated as always.